On the Ethode.com blog they've shared some hints for working with legacy code to help you more effectively refactor your way out of the "spaghetti code" you might have right now. These are more general tips and aren't really PHP (or even really web application) specific but they're a good starting place for any refactoring effort.

Legacy code is software that generates value for a business but is difficult for developers to change. [...] The longer this goes on, the more frustrated customers get with the software due to quirky defects, bad user experiences and long lead times for changes. Developers are afraid to make changes due to the "Jenga effect" -- as one piece of code is changed or removed, it often leads to new defects being introduced in the system in sometimes seemingly unrelated places. This compounds into what is known as "technical debt".

They continue on talking about what "spaghetti code" is, how it can happen and some of the warning signs you can use to determine just how far down the rabbit hole you and your code are. They talk about "The Big Rewrite" everyone dreams of but points out that this is almost never a practical path. Instead they offer some good things you can do to help fix the problem: quarantining the problem, refactoring relentlessly, keeping it simple and "doing the dishes" as you go rather than letting the changes pile up.